[SYNPY-1799, SYNPY-1804] Add manifest generation to sync_from_synapse

[danlu1]

Problem:

StorableContainer.sync_from_synapse() does not generate a manifest file after downloading content from Synapse. We want to add manifest generation similar to synapseutils.syncFromSynapse() so users can use that manifest for uploading data via sync_to_synapse.

Solution:

1. Added manifest CSV generation to StorableContainer.sync_from_synapse()
2. The manifest is written in CSV format using parentId and ID column names, consistent with the Synapse UI download cart and synapse get-download-list CLI output. Annotations and provenance are included as additional columns.
3. The implementation lives in three new helpers in storable_container.py:

• _extract_entity_metadata_for_manifest_csv() — extracts per-file rows and discovers annotation column keys dynamically

• _write_manifest_data_csv() — writes the CSV using DictWriter

• generate_manifest_csv() — public entry point, skips gracefully if path or files are absent

4. The protocol definition in storable_container_protocol.py was updated to keep the sync and async signatures in alignment.

Testing:

Unit tests and integration tests were added.

[Copilot]

Pull request overview

This PR adds manifest CSV generation to StorableContainer.sync_from_synapse() so downloaded content can be re-uploaded via sync_to_synapse using an interoperable manifest.csv format (matching Synapse UI download cart / CLI column naming).

Changes:

• Added manifest CSV helpers and integrated manifest generation into StorableContainer.sync_from_synapse_async() with manifest={all,root,suppress}.
• Deprecated legacy synapseutils.syncFromSynapse() to steer users to StorableContainer.sync_from_synapse.
• Added/updated unit tests around manifest behavior and the deprecation warning.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
synapseclient/models/mixins/storable_container.py	Adds CSV manifest generation helpers and hooks manifest generation into sync flow.
synapseclient/models/protocols/storable_container_protocol.py	Updates protocol signature/docs to include manifest parameter.
synapseutils/sync.py	Marks syncFromSynapse as deprecated with guidance to use StorableContainer.sync_from_synapse.
tests/unit/synapseclient/models/async/unit_test_folder_async.py	Adds tests for manifest behavior and CSV helper functions.
tests/unit/synapseutils/unit_test_synapseutils_sync.py	Adds a test asserting the deprecation warning is emitted.

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[andrewelamb]

Thanks @danlu1! I left some comments. You'll also need to update the docs folder:

• docs/tutorials/python/download_data_in_bulk.md: Use the new method
• docs/explanations/manifest_tsv.md: Don't make any changes here, this will be done in a different ticket